---
title: "PCA"
author: "Pierre Barry"
date: "`r format(Sys.time(), '%d %B, %Y, %H:%M')`"
output: 
  flexdashboard::flex_dashboard:
    theme: paper
    orientation: rows
    social: menu
    source_code: embed
    vertical_layout: scroll
    self_contained: false
---

```{r global, include=FALSE}
list.of.packages <- c("RColorBrewer","ggplot2","plotly")

for (i in list.of.packages){
  if (i %in% installed.packages()[,"Package"] == FALSE){
    install.packages(i)
  }
  eval(bquote(library(.(i))))
}
```

```{r, include = FALSE}
color_med_atl=data.frame(Location=c("Gulf of Lion","Costa Calida","Algarve","Bay of Biscay"),
                         Col=brewer.pal(n = 4, name = "RdBu"))
```

Alosa fallax {data-navmenu="Species"}
=======================================================================
  
```{r, include = FALSE}
load(file = paste(path,"/output/pca/Afall_PCA_list.Rdata",sep=""))
```

Row {.tabset data-height=100}
-----------------------
  
<center>

<font size="6">**Alosa fallax**</font>

</center>

Row {.tabset data-height=50}
-----------------------

<center>

<font size="6">**All filtered SNPS**</font>

</center>

Row {.tabset data-height=600}
-----------------------
  
### maf = 0
  
```{r}
pca=PCA_list$All_filtered$maf0[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",4),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",0)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))

p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.05

```{r}
pca=PCA_list$All_filtered$maf0.05[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",4),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",0)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.1

```{r}
pca=PCA_list$All_filtered$maf0.1[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",4),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",0)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.15

```{r}
pca=PCA_list$All_filtered$maf0.15[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",4),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",0)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.20

```{r}
pca=PCA_list$All_filtered$maf0.2[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",4),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",0)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.25

```{r}
pca=PCA_list$All_filtered$maf0.25[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",4),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",0)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.30

```{r}
pca=PCA_list$All_filtered$maf0.3[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",4),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",0)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.35

```{r}
pca=PCA_list$All_filtered$maf0.35[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",4),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",0)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.40

```{r}
pca=PCA_list$All_filtered$maf0.4[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",4),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",0)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.45

```{r}
pca=PCA_list$All_filtered$maf0.45[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",4),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",0)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.50

```{r}
pca=PCA_list$All_filtered$maf0.5[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",4),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",0)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

Row {.tabset data-height=50}
-----------------------
  
<center>

<font size="6">**Pruned filtered SNPS**</font>

</center>
  
Row {.tabset data-height=600}
-----------------------
  
### maf = 0
  
```{r}
pca=PCA_list$Prune_filtered$maf0[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",4),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",0)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.05

```{r}
pca=PCA_list$Prune_filtered$maf0.05[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",4),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",0)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.1

```{r}
pca=PCA_list$Prune_filtered$maf0.1[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",4),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",0)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.15

```{r}
pca=PCA_list$Prune_filtered$maf0.15[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",4),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",0)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.20

```{r}
pca=PCA_list$Prune_filtered$maf0.2[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",4),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",0)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.25

```{r}
pca=PCA_list$Prune_filtered$maf0.25[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",4),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",0)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.30

```{r}
pca=PCA_list$Prune_filtered$maf0.3[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",4),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",0)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.35

```{r}
pca=PCA_list$Prune_filtered$maf0.35[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",4),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",0)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.40

```{r}
pca=PCA_list$Prune_filtered$maf0.4[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",4),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",0)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.45

```{r}
pca=PCA_list$Prune_filtered$maf0.45[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",4),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",0)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.50

```{r}
pca=PCA_list$Prune_filtered$maf0.5[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",4),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",0)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

Row {.tabset data-height=50}
-----------------------
  
<center>

<font size="6">**All unfiltered SNPS**</font>

</center>
  
Row {.tabset data-height=600}
-----------------------
  
### maf = 0
  
```{r}
pca=PCA_list$All_unfiltered$maf0[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",4),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",0)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.05

```{r}
pca=PCA_list$All_unfiltered$maf0.05[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",4),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",0)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.1

```{r}
pca=PCA_list$All_unfiltered$maf0.1[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",4),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",0)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.15

```{r}
pca=PCA_list$All_unfiltered$maf0.15[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",4),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",0)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.20

```{r}
pca=PCA_list$All_unfiltered$maf0.2[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",4),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",0)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.25

```{r}
pca=PCA_list$All_unfiltered$maf0.25[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",4),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",0)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.30

```{r}
pca=PCA_list$All_unfiltered$maf0.3[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",4),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",0)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.35

```{r}
pca=PCA_list$All_unfiltered$maf0.35[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",4),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",0)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.40

```{r}
pca=PCA_list$All_unfiltered$maf0.4[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",4),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",0)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.45

```{r}
pca=PCA_list$All_unfiltered$maf0.45[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",4),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",0)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.50

```{r}
pca=PCA_list$All_unfiltered$maf0.5[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",4),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",0)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

Row {.tabset data-height=50}
-----------------------
  
<center>

<font size="6">**Pruned unfiltered SNPS**</font>

</center>
  
Row {.tabset data-height=600}
-----------------------
  
### maf = 0
  
```{r}
pca=PCA_list$Prune_unfiltered$maf0[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",4),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",0)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.05

```{r}
pca=PCA_list$Prune_unfiltered$maf0.05[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",4),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",0)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.1

```{r}
pca=PCA_list$Prune_unfiltered$maf0.1[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",4),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",0)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.15

```{r}
pca=PCA_list$Prune_unfiltered$maf0.15[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",4),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",0)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.20

```{r}
pca=PCA_list$Prune_unfiltered$maf0.2[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",4),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",0)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.25

```{r}
pca=PCA_list$Prune_unfiltered$maf0.25[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",4),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",0)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.30

```{r}
pca=PCA_list$Prune_unfiltered$maf0.3[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",4),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",0)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.35

```{r}
pca=PCA_list$Prune_unfiltered$maf0.35[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",4),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",0)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.40

```{r}
pca=PCA_list$Prune_unfiltered$maf0.4[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",4),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",0)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.45

```{r}
pca=PCA_list$Prune_unfiltered$maf0.45[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",4),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",0)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.50

```{r}
pca=PCA_list$Prune_unfiltered$maf0.5[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",4),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",0)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```


Coryphoblennius galerita {data-navmenu="Species"}
=======================================================================
  
```{r, include = FALSE}
load(file = paste(path,"/output/pca/Cgale_PCA_list.Rdata",sep=""))
```

Row {.tabset data-height=100}
-----------------------
  
<center>

<font size="6">**Coryphoblennius galerita**</font>

</center>

Row {.tabset data-height=50}
-----------------------

<center>

<font size="6">**All filtered SNPS**</font>

</center>

Row {.tabset data-height=600}
-----------------------
  
### maf = 0
  
```{r}
pca=PCA_list$All_filtered$maf0[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.05

```{r}
pca=PCA_list$All_filtered$maf0.05[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.1

```{r}
pca=PCA_list$All_filtered$maf0.1[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.15

```{r}
pca=PCA_list$All_filtered$maf0.15[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.20

```{r}
pca=PCA_list$All_filtered$maf0.2[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.25

```{r}
pca=PCA_list$All_filtered$maf0.25[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.30

```{r}
pca=PCA_list$All_filtered$maf0.3[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.35

```{r}
pca=PCA_list$All_filtered$maf0.35[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.40

```{r}
pca=PCA_list$All_filtered$maf0.4[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.45

```{r}
pca=PCA_list$All_filtered$maf0.45[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.50

```{r}
pca=PCA_list$All_filtered$maf0.5[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

Row {.tabset data-height=50}
-----------------------
  
<center>

<font size="6">**Pruned filtered SNPS**</font>

</center>
  
Row {.tabset data-height=600}
-----------------------
  
### maf = 0
  
```{r}
pca=PCA_list$Prune_filtered$maf0[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.05

```{r}
pca=PCA_list$Prune_filtered$maf0.05[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.1

```{r}
pca=PCA_list$Prune_filtered$maf0.1[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.15

```{r}
pca=PCA_list$Prune_filtered$maf0.15[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.20

```{r}
pca=PCA_list$Prune_filtered$maf0.2[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.25

```{r}
pca=PCA_list$Prune_filtered$maf0.25[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.30

```{r}
pca=PCA_list$Prune_filtered$maf0.3[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.35

```{r}
pca=PCA_list$Prune_filtered$maf0.35[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.40

```{r}
pca=PCA_list$Prune_filtered$maf0.4[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.45

```{r}
pca=PCA_list$Prune_filtered$maf0.45[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.50

```{r}
pca=PCA_list$Prune_filtered$maf0.5[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

Row {.tabset data-height=50}
-----------------------
  
<center>

<font size="6">**All unfiltered SNPS**</font>

</center>
  
Row {.tabset data-height=600}
-----------------------
  
### maf = 0
  
```{r}
pca=PCA_list$All_unfiltered$maf0[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.05

```{r}
pca=PCA_list$All_unfiltered$maf0.05[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.1

```{r}
pca=PCA_list$All_unfiltered$maf0.1[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.15

```{r}
pca=PCA_list$All_unfiltered$maf0.15[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.20

```{r}
pca=PCA_list$All_unfiltered$maf0.2[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.25

```{r}
pca=PCA_list$All_unfiltered$maf0.25[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.30

```{r}
pca=PCA_list$All_unfiltered$maf0.3[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.35

```{r}
pca=PCA_list$All_unfiltered$maf0.35[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.40

```{r}
pca=PCA_list$All_unfiltered$maf0.4[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.45

```{r}
pca=PCA_list$All_unfiltered$maf0.45[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.50

```{r}
pca=PCA_list$All_unfiltered$maf0.5[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

Row {.tabset data-height=50}
-----------------------
  
<center>

<font size="6">**Pruned unfiltered SNPS**</font>

</center>
  
Row {.tabset data-height=600}
-----------------------
  
### maf = 0
  
```{r}
pca=PCA_list$Prune_unfiltered$maf0[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.05

```{r}
pca=PCA_list$Prune_unfiltered$maf0.05[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.1

```{r}
pca=PCA_list$Prune_unfiltered$maf0.1[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.15

```{r}
pca=PCA_list$Prune_unfiltered$maf0.15[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.20

```{r}
pca=PCA_list$Prune_unfiltered$maf0.2[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.25

```{r}
pca=PCA_list$Prune_unfiltered$maf0.25[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.30

```{r}
pca=PCA_list$Prune_unfiltered$maf0.3[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.35

```{r}
pca=PCA_list$Prune_unfiltered$maf0.35[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.40

```{r}
pca=PCA_list$Prune_unfiltered$maf0.4[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.45

```{r}
pca=PCA_list$Prune_unfiltered$maf0.45[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.50

```{r}
pca=PCA_list$Prune_unfiltered$maf0.5[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

Dicentrarchus labrax {data-navmenu="Species"}
=======================================================================
  
```{r, include = FALSE}
load(file = paste(path,"/output/pca/Dlabr_PCA_list.Rdata",sep=""))
```

Row {.tabset data-height=100}
-----------------------
  
<center>

<font size="6">**Dicentrarchus labrax**</font>

</center>
  
Row {.tabset data-height=50}
-----------------------

<center>

<font size="6">**All filtered SNPS**</font>

</center>

Row {.tabset data-height=600}
-----------------------
  
### maf = 0
  
```{r}
pca=PCA_list$All_filtered$maf0[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.05

```{r}
pca=PCA_list$All_filtered$maf0.05[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.1

```{r}
pca=PCA_list$All_filtered$maf0.1[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.15

```{r}
pca=PCA_list$All_filtered$maf0.15[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.20

```{r}
pca=PCA_list$All_filtered$maf0.2[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.25

```{r}
pca=PCA_list$All_filtered$maf0.25[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.30

```{r}
pca=PCA_list$All_filtered$maf0.3[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.35

```{r}
pca=PCA_list$All_filtered$maf0.35[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.40

```{r}
pca=PCA_list$All_filtered$maf0.4[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.45

```{r}
pca=PCA_list$All_filtered$maf0.45[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.50

```{r}
pca=PCA_list$All_filtered$maf0.5[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

Row {.tabset data-height=50}
-----------------------
  
<center>

<font size="6">**Pruned filtered SNPS**</font>

</center>
  
Row {.tabset data-height=600}
-----------------------
  
### maf = 0
  
```{r}
pca=PCA_list$Prune_filtered$maf0[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.05

```{r}
pca=PCA_list$Prune_filtered$maf0.05[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.1

```{r}
pca=PCA_list$Prune_filtered$maf0.1[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.15

```{r}
pca=PCA_list$Prune_filtered$maf0.15[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.20

```{r}
pca=PCA_list$Prune_filtered$maf0.2[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.25

```{r}
pca=PCA_list$Prune_filtered$maf0.25[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.30

```{r}
pca=PCA_list$Prune_filtered$maf0.3[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.35

```{r}
pca=PCA_list$Prune_filtered$maf0.35[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.40

```{r}
pca=PCA_list$Prune_filtered$maf0.4[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.45

```{r}
pca=PCA_list$Prune_filtered$maf0.45[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.50

```{r}
pca=PCA_list$Prune_filtered$maf0.5[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

Row {.tabset data-height=50}
-----------------------
  
<center>

<font size="6">**All unfiltered SNPS**</font>

</center>
  
Row {.tabset data-height=600}
-----------------------
  
### maf = 0
  
```{r}
pca=PCA_list$All_unfiltered$maf0[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.05

```{r}
pca=PCA_list$All_unfiltered$maf0.05[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.1

```{r}
pca=PCA_list$All_unfiltered$maf0.1[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.15

```{r}
pca=PCA_list$All_unfiltered$maf0.15[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.20

```{r}
pca=PCA_list$All_unfiltered$maf0.2[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.25

```{r}
pca=PCA_list$All_unfiltered$maf0.25[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.30

```{r}
pca=PCA_list$All_unfiltered$maf0.3[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.35

```{r}
pca=PCA_list$All_unfiltered$maf0.35[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.40

```{r}
pca=PCA_list$All_unfiltered$maf0.4[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.45

```{r}
pca=PCA_list$All_unfiltered$maf0.45[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.50

```{r}
pca=PCA_list$All_unfiltered$maf0.5[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

Row {.tabset data-height=50}
-----------------------
  
<center>

<font size="6">**Pruned unfiltered SNPS**</font>

</center>
  
Row {.tabset data-height=600}
-----------------------
  
### maf = 0
  
```{r}
pca=PCA_list$Prune_unfiltered$maf0[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.05

```{r}
pca=PCA_list$Prune_unfiltered$maf0.05[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.1

```{r}
pca=PCA_list$Prune_unfiltered$maf0.1[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.15

```{r}
pca=PCA_list$Prune_unfiltered$maf0.15[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.20

```{r}
pca=PCA_list$Prune_unfiltered$maf0.2[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.25

```{r}
pca=PCA_list$Prune_unfiltered$maf0.25[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.30

```{r}
pca=PCA_list$Prune_unfiltered$maf0.3[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.35

```{r}
pca=PCA_list$Prune_unfiltered$maf0.35[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.40

```{r}
pca=PCA_list$Prune_unfiltered$maf0.4[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.45

```{r}
pca=PCA_list$Prune_unfiltered$maf0.45[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.50

```{r}
pca=PCA_list$Prune_unfiltered$maf0.5[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

Hippocampus guttulatus {data-navmenu="Species"}
=======================================================================

```{r, include = FALSE}
load(file = paste(path,"/output/pca/Hgutt_PCA_list.Rdata",sep=""))
```

Row {.tabset data-height=100}
-----------------------
  
<center>

<font size="6">**Hippocampus guttulatus**</font>

</center>

Row {.tabset data-height=50}
-----------------------

<center>

<font size="6">**All filtered SNPS**</font>

</center>

Row {.tabset data-height=600}
-----------------------

### maf = 0

```{r}
pca=PCA_list$All_filtered$maf0[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",11),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.05

```{r}
pca=PCA_list$All_filtered$maf0.05[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",11),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.1

```{r}
pca=PCA_list$All_filtered$maf0.1[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",11),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.15

```{r}
pca=PCA_list$All_filtered$maf0.15[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",11),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.20

```{r}
pca=PCA_list$All_filtered$maf0.2[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",11),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.25

```{r}
pca=PCA_list$All_filtered$maf0.25[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",11),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.30

```{r}
pca=PCA_list$All_filtered$maf0.3[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",11),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.35

```{r}
pca=PCA_list$All_filtered$maf0.35[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",11),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.40

```{r}
pca=PCA_list$All_filtered$maf0.4[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",11),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.45

```{r}
pca=PCA_list$All_filtered$maf0.45[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",11),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.50

```{r}
pca=PCA_list$All_filtered$maf0.5[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",11),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

Row {.tabset data-height=50}
-----------------------

<center>

<font size="6">**Pruned filtered SNPS**</font>

</center>

Row {.tabset data-height=600}
-----------------------

### maf = 0

```{r}
pca=PCA_list$Prune_filtered$maf0[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",11),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.05

```{r}
pca=PCA_list$Prune_filtered$maf0.05[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",11),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.1

```{r}
pca=PCA_list$Prune_filtered$maf0.1[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",11),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.15

```{r}
pca=PCA_list$Prune_filtered$maf0.15[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",11),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.20

```{r}
pca=PCA_list$Prune_filtered$maf0.2[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",11),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.25

```{r}
pca=PCA_list$Prune_filtered$maf0.25[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",11),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.30

```{r}
pca=PCA_list$Prune_filtered$maf0.3[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",11),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.35

```{r}
pca=PCA_list$Prune_filtered$maf0.35[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",11),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.40

```{r}
pca=PCA_list$Prune_filtered$maf0.4[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",11),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.45

```{r}
pca=PCA_list$Prune_filtered$maf0.45[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",11),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.50

```{r}
pca=PCA_list$Prune_filtered$maf0.5[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",11),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

Row {.tabset data-height=50}
-----------------------

<center>

<font size="6">**All unfiltered SNPS**</font>

</center>

Row {.tabset data-height=600}
-----------------------

### maf = 0

```{r}
pca=PCA_list$All_unfiltered$maf0[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",11),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.05

```{r}
pca=PCA_list$All_unfiltered$maf0.05[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",11),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.1

```{r}
pca=PCA_list$All_unfiltered$maf0.1[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",11),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.15

```{r}
pca=PCA_list$All_unfiltered$maf0.15[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",11),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.20

```{r}
pca=PCA_list$All_unfiltered$maf0.2[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",11),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.25

```{r}
pca=PCA_list$All_unfiltered$maf0.25[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",11),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.30

```{r}
pca=PCA_list$All_unfiltered$maf0.3[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",11),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.35

```{r}
pca=PCA_list$All_unfiltered$maf0.35[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",11),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.40

```{r}
pca=PCA_list$All_unfiltered$maf0.4[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",11),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.45

```{r}
pca=PCA_list$All_unfiltered$maf0.45[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",11),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.50

```{r}
pca=PCA_list$All_unfiltered$maf0.5[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",11),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

Row {.tabset data-height=50}
-----------------------

<center>

<font size="6">**Pruned unfiltered SNPS**</font>

</center>

Row {.tabset data-height=600}
-----------------------

### maf = 0

```{r}
pca=PCA_list$Prune_unfiltered$maf0[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",11),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.05

```{r}
pca=PCA_list$Prune_unfiltered$maf0.05[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",11),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.1

```{r}
pca=PCA_list$Prune_unfiltered$maf0.1[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",11),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.15

```{r}
pca=PCA_list$Prune_unfiltered$maf0.15[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",11),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.20

```{r}
pca=PCA_list$Prune_unfiltered$maf0.2[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",11),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.25

```{r}
pca=PCA_list$Prune_unfiltered$maf0.25[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",11),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.30

```{r}
pca=PCA_list$Prune_unfiltered$maf0.3[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",11),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.35

```{r}
pca=PCA_list$Prune_unfiltered$maf0.35[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",11),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.40

```{r}
pca=PCA_list$Prune_unfiltered$maf0.4[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",11),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.45

```{r}
pca=PCA_list$Prune_unfiltered$maf0.45[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",11),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.50

```{r}
pca=PCA_list$Prune_unfiltered$maf0.5[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",11),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

Merluccius merluccius {data-navmenu="Species"}
=======================================================================
  
```{r, include = FALSE}
load(file = paste(path,"/output/pca/Mmerl_PCA_list.Rdata",sep=""))
```

Row {.tabset data-height=100}
-----------------------
  
<center>

<font size="6">**Merluccius merluccius**</font>

</center>
  
Row {.tabset data-height=50}
-----------------------

<center>

<font size="6">**All filtered SNPS**</font>

</center>

Row {.tabset data-height=600}
-----------------------
  
### maf = 0
  
```{r}
pca=PCA_list$All_filtered$maf0[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.05

```{r}
pca=PCA_list$All_filtered$maf0.05[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.1

```{r}
pca=PCA_list$All_filtered$maf0.1[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.15

```{r}
pca=PCA_list$All_filtered$maf0.15[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.20

```{r}
pca=PCA_list$All_filtered$maf0.2[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.25

```{r}
pca=PCA_list$All_filtered$maf0.25[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.30

```{r}
pca=PCA_list$All_filtered$maf0.3[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.35

```{r}
pca=PCA_list$All_filtered$maf0.35[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.40

```{r}
pca=PCA_list$All_filtered$maf0.4[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.45

```{r}
pca=PCA_list$All_filtered$maf0.45[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.50

```{r}
pca=PCA_list$All_filtered$maf0.5[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

Row {.tabset data-height=50}
-----------------------
  
<center>

<font size="6">**Pruned filtered SNPS**</font>

</center>
  
Row {.tabset data-height=600}
-----------------------
  
### maf = 0
  
```{r}
pca=PCA_list$Prune_filtered$maf0[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.05

```{r}
pca=PCA_list$Prune_filtered$maf0.05[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.1

```{r}
pca=PCA_list$Prune_filtered$maf0.1[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.15

```{r}
pca=PCA_list$Prune_filtered$maf0.15[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.20

```{r}
pca=PCA_list$Prune_filtered$maf0.2[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.25

```{r}
pca=PCA_list$Prune_filtered$maf0.25[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.30

```{r}
pca=PCA_list$Prune_filtered$maf0.3[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.35

```{r}
pca=PCA_list$Prune_filtered$maf0.35[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.40

```{r}
pca=PCA_list$Prune_filtered$maf0.4[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.45

```{r}
pca=PCA_list$Prune_filtered$maf0.45[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.50

```{r}
pca=PCA_list$Prune_filtered$maf0.5[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

Row {.tabset data-height=50}
-----------------------
  
<center>

<font size="6">**All unfiltered SNPS**</font>

</center>
  
Row {.tabset data-height=600}
-----------------------
  
### maf = 0
  
```{r}
pca=PCA_list$All_unfiltered$maf0[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.05

```{r}
pca=PCA_list$All_unfiltered$maf0.05[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.1

```{r}
pca=PCA_list$All_unfiltered$maf0.1[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.15

```{r}
pca=PCA_list$All_unfiltered$maf0.15[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.20

```{r}
pca=PCA_list$All_unfiltered$maf0.2[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.25

```{r}
pca=PCA_list$All_unfiltered$maf0.25[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.30

```{r}
pca=PCA_list$All_unfiltered$maf0.3[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.35

```{r}
pca=PCA_list$All_unfiltered$maf0.35[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.40

```{r}
pca=PCA_list$All_unfiltered$maf0.4[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.45

```{r}
pca=PCA_list$All_unfiltered$maf0.45[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.50

```{r}
pca=PCA_list$All_unfiltered$maf0.5[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

Row {.tabset data-height=50}
-----------------------
  
<center>

<font size="6">**Pruned unfiltered SNPS**</font>

</center>
  
Row {.tabset data-height=600}
-----------------------
  
### maf = 0
  
```{r}
pca=PCA_list$Prune_unfiltered$maf0[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.05

```{r}
pca=PCA_list$Prune_unfiltered$maf0.05[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.1

```{r}
pca=PCA_list$Prune_unfiltered$maf0.1[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.15

```{r}
pca=PCA_list$Prune_unfiltered$maf0.15[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.20

```{r}
pca=PCA_list$Prune_unfiltered$maf0.2[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.25

```{r}
pca=PCA_list$Prune_unfiltered$maf0.25[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.30

```{r}
pca=PCA_list$Prune_unfiltered$maf0.3[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.35

```{r}
pca=PCA_list$Prune_unfiltered$maf0.35[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.40

```{r}
pca=PCA_list$Prune_unfiltered$maf0.4[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.45

```{r}
pca=PCA_list$Prune_unfiltered$maf0.45[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.50

```{r}
pca=PCA_list$Prune_unfiltered$maf0.5[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

Mullus surmuletus {data-navmenu="Species"}
=======================================================================
  
```{r, include = FALSE}
load(file = paste(path,"/output/pca/Msurm_PCA_list.Rdata",sep=""))
```

Row {.tabset data-height=100}
-----------------------
  
<center>

<font size="6">**Mullus surmuletus**</font>

</center>
  
Row {.tabset data-height=50}
-----------------------

<center>

<font size="6">**All filtered SNPS**</font>

</center>

Row {.tabset data-height=600}
-----------------------
  
### maf = 0
  
```{r}
pca=PCA_list$All_filtered$maf0[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.05

```{r}
pca=PCA_list$All_filtered$maf0.05[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.1

```{r}
pca=PCA_list$All_filtered$maf0.1[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.15

```{r}
pca=PCA_list$All_filtered$maf0.15[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.20

```{r}
pca=PCA_list$All_filtered$maf0.2[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.25

```{r}
pca=PCA_list$All_filtered$maf0.25[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.30

```{r}
pca=PCA_list$All_filtered$maf0.3[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.35

```{r}
pca=PCA_list$All_filtered$maf0.35[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.40

```{r}
pca=PCA_list$All_filtered$maf0.4[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.45

```{r}
pca=PCA_list$All_filtered$maf0.45[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.50

```{r}
pca=PCA_list$All_filtered$maf0.5[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

Row {.tabset data-height=50}
-----------------------
  
<center>

<font size="6">**Pruned filtered SNPS**</font>

</center>
  
Row {.tabset data-height=600}
-----------------------
  
### maf = 0
  
```{r}
pca=PCA_list$Prune_filtered$maf0[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.05

```{r}
pca=PCA_list$Prune_filtered$maf0.05[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.1

```{r}
pca=PCA_list$Prune_filtered$maf0.1[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.15

```{r}
pca=PCA_list$Prune_filtered$maf0.15[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.20

```{r}
pca=PCA_list$Prune_filtered$maf0.2[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.25

```{r}
pca=PCA_list$Prune_filtered$maf0.25[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.30

```{r}
pca=PCA_list$Prune_filtered$maf0.3[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.35

```{r}
pca=PCA_list$Prune_filtered$maf0.35[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.40

```{r}
pca=PCA_list$Prune_filtered$maf0.4[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.45

```{r}
pca=PCA_list$Prune_filtered$maf0.45[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.50

```{r}
pca=PCA_list$Prune_filtered$maf0.5[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

Row {.tabset data-height=50}
-----------------------
  
<center>

<font size="6">**All unfiltered SNPS**</font>

</center>
  
Row {.tabset data-height=600}
-----------------------
  
### maf = 0
  
```{r}
pca=PCA_list$All_unfiltered$maf0[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.05

```{r}
pca=PCA_list$All_unfiltered$maf0.05[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.1

```{r}
pca=PCA_list$All_unfiltered$maf0.1[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.15

```{r}
pca=PCA_list$All_unfiltered$maf0.15[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.20

```{r}
pca=PCA_list$All_unfiltered$maf0.2[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.25

```{r}
pca=PCA_list$All_unfiltered$maf0.25[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.30

```{r}
pca=PCA_list$All_unfiltered$maf0.3[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.35

```{r}
pca=PCA_list$All_unfiltered$maf0.35[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.40

```{r}
pca=PCA_list$All_unfiltered$maf0.4[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.45

```{r}
pca=PCA_list$All_unfiltered$maf0.45[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.50

```{r}
pca=PCA_list$All_unfiltered$maf0.5[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

Row {.tabset data-height=50}
-----------------------
  
<center>

<font size="6">**Pruned unfiltered SNPS**</font>

</center>
  
Row {.tabset data-height=600}
-----------------------
  
### maf = 0
  
```{r}
pca=PCA_list$Prune_unfiltered$maf0[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.05

```{r}
pca=PCA_list$Prune_unfiltered$maf0.05[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.1

```{r}
pca=PCA_list$Prune_unfiltered$maf0.1[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.15

```{r}
pca=PCA_list$Prune_unfiltered$maf0.15[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.20

```{r}
pca=PCA_list$Prune_unfiltered$maf0.2[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.25

```{r}
pca=PCA_list$Prune_unfiltered$maf0.25[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.30

```{r}
pca=PCA_list$Prune_unfiltered$maf0.3[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.35

```{r}
pca=PCA_list$Prune_unfiltered$maf0.35[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.40

```{r}
pca=PCA_list$Prune_unfiltered$maf0.4[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.45

```{r}
pca=PCA_list$Prune_unfiltered$maf0.45[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.50

```{r}
pca=PCA_list$Prune_unfiltered$maf0.5[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

Serranus cabrilla {data-navmenu="Species"}
=======================================================================
  
```{r, include = FALSE}
load(file = paste(path,"/output/pca/Scabr_PCA_list.Rdata",sep=""))
```

Row {.tabset data-height=100}
-----------------------
  
<center>

<font size="6">**Serranus cabrilla**</font>

</center>
  
Row {.tabset data-height=50}
-----------------------

<center>

<font size="6">**All filtered SNPS**</font>

</center>

Row {.tabset data-height=600}
-----------------------
  
### maf = 0
  
```{r}
pca=PCA_list$All_filtered$maf0[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.05

```{r}
pca=PCA_list$All_filtered$maf0.05[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.1

```{r}
pca=PCA_list$All_filtered$maf0.1[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.15

```{r}
pca=PCA_list$All_filtered$maf0.15[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.20

```{r}
pca=PCA_list$All_filtered$maf0.2[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.25

```{r}
pca=PCA_list$All_filtered$maf0.25[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.30

```{r}
pca=PCA_list$All_filtered$maf0.3[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.35

```{r}
pca=PCA_list$All_filtered$maf0.35[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.40

```{r}
pca=PCA_list$All_filtered$maf0.4[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.45

```{r}
pca=PCA_list$All_filtered$maf0.45[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.50

```{r}
pca=PCA_list$All_filtered$maf0.5[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

Row {.tabset data-height=50}
-----------------------
  
<center>

<font size="6">**Pruned filtered SNPS**</font>

</center>
  
Row {.tabset data-height=600}
-----------------------
  
### maf = 0
  
```{r}
pca=PCA_list$Prune_filtered$maf0[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.05

```{r}
pca=PCA_list$Prune_filtered$maf0.05[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.1

```{r}
pca=PCA_list$Prune_filtered$maf0.1[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.15

```{r}
pca=PCA_list$Prune_filtered$maf0.15[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.20

```{r}
pca=PCA_list$Prune_filtered$maf0.2[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.25

```{r}
pca=PCA_list$Prune_filtered$maf0.25[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.30

```{r}
pca=PCA_list$Prune_filtered$maf0.3[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.35

```{r}
pca=PCA_list$Prune_filtered$maf0.35[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.40

```{r}
pca=PCA_list$Prune_filtered$maf0.4[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.45

```{r}
pca=PCA_list$Prune_filtered$maf0.45[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.50

```{r}
pca=PCA_list$Prune_filtered$maf0.5[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

Row {.tabset data-height=50}
-----------------------
  
<center>

<font size="6">**All unfiltered SNPS**</font>

</center>
  
Row {.tabset data-height=600}
-----------------------
  
### maf = 0
  
```{r}
pca=PCA_list$All_unfiltered$maf0[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.05

```{r}
pca=PCA_list$All_unfiltered$maf0.05[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.1

```{r}
pca=PCA_list$All_unfiltered$maf0.1[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.15

```{r}
pca=PCA_list$All_unfiltered$maf0.15[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.20

```{r}
pca=PCA_list$All_unfiltered$maf0.2[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.25

```{r}
pca=PCA_list$All_unfiltered$maf0.25[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.30

```{r}
pca=PCA_list$All_unfiltered$maf0.3[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.35

```{r}
pca=PCA_list$All_unfiltered$maf0.35[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.40

```{r}
pca=PCA_list$All_unfiltered$maf0.4[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.45

```{r}
pca=PCA_list$All_unfiltered$maf0.45[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.50

```{r}
pca=PCA_list$All_unfiltered$maf0.5[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

Row {.tabset data-height=50}
-----------------------
  
<center>

<font size="6">**Pruned unfiltered SNPS**</font>

</center>
  
Row {.tabset data-height=600}
-----------------------
  
### maf = 0
  
```{r}
pca=PCA_list$Prune_unfiltered$maf0[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.05

```{r}
pca=PCA_list$Prune_unfiltered$maf0.05[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.1

```{r}
pca=PCA_list$Prune_unfiltered$maf0.1[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.15

```{r}
pca=PCA_list$Prune_unfiltered$maf0.15[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.20

```{r}
pca=PCA_list$Prune_unfiltered$maf0.2[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.25

```{r}
pca=PCA_list$Prune_unfiltered$maf0.25[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.30

```{r}
pca=PCA_list$Prune_unfiltered$maf0.3[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.35

```{r}
pca=PCA_list$Prune_unfiltered$maf0.35[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.40

```{r}
pca=PCA_list$Prune_unfiltered$maf0.4[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.45

```{r}
pca=PCA_list$Prune_unfiltered$maf0.45[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.50

```{r}
pca=PCA_list$Prune_unfiltered$maf0.5[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

Spondyliosoma cantharus {data-navmenu="Species"}
=======================================================================
  
```{r, include = FALSE}
load(file = paste(path,"/output/pca/Scant_PCA_list.Rdata",sep=""))
```

Row {.tabset data-height=100}
-----------------------
  
<center>

<font size="6">**Spondyliosoma cantharus**</font>

</center>
  
Row {.tabset data-height=50}
-----------------------

<center>

<font size="6">**All filtered SNPS**</font>

</center>

Row {.tabset data-height=600}
-----------------------
  
### maf = 0
  
```{r}
pca=PCA_list$All_filtered$maf0[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.05

```{r}
pca=PCA_list$All_filtered$maf0.05[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.1

```{r}
pca=PCA_list$All_filtered$maf0.1[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.15

```{r}
pca=PCA_list$All_filtered$maf0.15[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.20

```{r}
pca=PCA_list$All_filtered$maf0.2[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.25

```{r}
pca=PCA_list$All_filtered$maf0.25[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.30

```{r}
pca=PCA_list$All_filtered$maf0.3[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.35

```{r}
pca=PCA_list$All_filtered$maf0.35[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.40

```{r}
pca=PCA_list$All_filtered$maf0.4[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.45

```{r}
pca=PCA_list$All_filtered$maf0.45[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.50

```{r}
pca=PCA_list$All_filtered$maf0.5[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

Row {.tabset data-height=50}
-----------------------
  
<center>

<font size="6">**Pruned filtered SNPS**</font>

</center>
  
Row {.tabset data-height=600}
-----------------------
  
### maf = 0
  
```{r}
pca=PCA_list$Prune_filtered$maf0[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.05

```{r}
pca=PCA_list$Prune_filtered$maf0.05[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.1

```{r}
pca=PCA_list$Prune_filtered$maf0.1[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.15

```{r}
pca=PCA_list$Prune_filtered$maf0.15[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.20

```{r}
pca=PCA_list$Prune_filtered$maf0.2[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.25

```{r}
pca=PCA_list$Prune_filtered$maf0.25[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.30

```{r}
pca=PCA_list$Prune_filtered$maf0.3[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.35

```{r}
pca=PCA_list$Prune_filtered$maf0.35[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.40

```{r}
pca=PCA_list$Prune_filtered$maf0.4[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.45

```{r}
pca=PCA_list$Prune_filtered$maf0.45[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.50

```{r}
pca=PCA_list$Prune_filtered$maf0.5[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

Row {.tabset data-height=50}
-----------------------
  
<center>

<font size="6">**All unfiltered SNPS**</font>

</center>
  
Row {.tabset data-height=600}
-----------------------
  
### maf = 0
  
```{r}
pca=PCA_list$All_unfiltered$maf0[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.05

```{r}
pca=PCA_list$All_unfiltered$maf0.05[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.1

```{r}
pca=PCA_list$All_unfiltered$maf0.1[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.15

```{r}
pca=PCA_list$All_unfiltered$maf0.15[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.20

```{r}
pca=PCA_list$All_unfiltered$maf0.2[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.25

```{r}
pca=PCA_list$All_unfiltered$maf0.25[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.30

```{r}
pca=PCA_list$All_unfiltered$maf0.3[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.35

```{r}
pca=PCA_list$All_unfiltered$maf0.35[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.40

```{r}
pca=PCA_list$All_unfiltered$maf0.4[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.45

```{r}
pca=PCA_list$All_unfiltered$maf0.45[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.50

```{r}
pca=PCA_list$All_unfiltered$maf0.5[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

Row {.tabset data-height=50}
-----------------------
  
<center>

<font size="6">**Pruned unfiltered SNPS**</font>

</center>
  
Row {.tabset data-height=600}
-----------------------
  
### maf = 0
  
```{r}
pca=PCA_list$Prune_unfiltered$maf0[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.05

```{r}
pca=PCA_list$Prune_unfiltered$maf0.05[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.1

```{r}
pca=PCA_list$Prune_unfiltered$maf0.1[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.15

```{r}
pca=PCA_list$Prune_unfiltered$maf0.15[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.20

```{r}
pca=PCA_list$Prune_unfiltered$maf0.2[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.25

```{r}
pca=PCA_list$Prune_unfiltered$maf0.25[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.30

```{r}
pca=PCA_list$Prune_unfiltered$maf0.3[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.35

```{r}
pca=PCA_list$Prune_unfiltered$maf0.35[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.40

```{r}
pca=PCA_list$Prune_unfiltered$maf0.4[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.45

```{r}
pca=PCA_list$Prune_unfiltered$maf0.45[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.50

```{r}
pca=PCA_list$Prune_unfiltered$maf0.5[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

Symphodus cinereus {data-navmenu="Species"}
=======================================================================
  
```{r, include = FALSE}
load(file = paste(path,"/output/pca/Scine_PCA_list.Rdata",sep=""))
```

Row {.tabset data-height=100}
-----------------------
  
<center>

<font size="6">**Symphodus cinereus**</font>

</center>
  
Row {.tabset data-height=50}
-----------------------

<center>

<font size="6">**All filtered SNPS**</font>

</center>

Row {.tabset data-height=600}
-----------------------
  
### maf = 0
  
```{r}
pca=PCA_list$All_filtered$maf0[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.05

```{r}
pca=PCA_list$All_filtered$maf0.05[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.1

```{r}
pca=PCA_list$All_filtered$maf0.1[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.15

```{r}
pca=PCA_list$All_filtered$maf0.15[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.20

```{r}
pca=PCA_list$All_filtered$maf0.2[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.25

```{r}
pca=PCA_list$All_filtered$maf0.25[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.30

```{r}
pca=PCA_list$All_filtered$maf0.3[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.35

```{r}
pca=PCA_list$All_filtered$maf0.35[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.40

```{r}
pca=PCA_list$All_filtered$maf0.4[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.45

```{r}
pca=PCA_list$All_filtered$maf0.45[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.50

```{r}
pca=PCA_list$All_filtered$maf0.5[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

Row {.tabset data-height=50}
-----------------------
  
<center>

<font size="6">**Pruned filtered SNPS**</font>

</center>
  
Row {.tabset data-height=600}
-----------------------
  
### maf = 0
  
```{r}
pca=PCA_list$Prune_filtered$maf0[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.05

```{r}
pca=PCA_list$Prune_filtered$maf0.05[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.1

```{r}
pca=PCA_list$Prune_filtered$maf0.1[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.15

```{r}
pca=PCA_list$Prune_filtered$maf0.15[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.20

```{r}
pca=PCA_list$Prune_filtered$maf0.2[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.25

```{r}
pca=PCA_list$Prune_filtered$maf0.25[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.30

```{r}
pca=PCA_list$Prune_filtered$maf0.3[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.35

```{r}
pca=PCA_list$Prune_filtered$maf0.35[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.40

```{r}
pca=PCA_list$Prune_filtered$maf0.4[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.45

```{r}
pca=PCA_list$Prune_filtered$maf0.45[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.50

```{r}
pca=PCA_list$Prune_filtered$maf0.5[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

Row {.tabset data-height=50}
-----------------------
  
<center>

<font size="6">**All unfiltered SNPS**</font>

</center>
  
Row {.tabset data-height=600}
-----------------------
  
### maf = 0
  
```{r}
pca=PCA_list$All_unfiltered$maf0[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.05

```{r}
pca=PCA_list$All_unfiltered$maf0.05[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.1

```{r}
pca=PCA_list$All_unfiltered$maf0.1[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.15

```{r}
pca=PCA_list$All_unfiltered$maf0.15[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.20

```{r}
pca=PCA_list$All_unfiltered$maf0.2[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.25

```{r}
pca=PCA_list$All_unfiltered$maf0.25[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.30

```{r}
pca=PCA_list$All_unfiltered$maf0.3[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.35

```{r}
pca=PCA_list$All_unfiltered$maf0.35[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.40

```{r}
pca=PCA_list$All_unfiltered$maf0.4[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.45

```{r}
pca=PCA_list$All_unfiltered$maf0.45[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.50

```{r}
pca=PCA_list$All_unfiltered$maf0.5[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

Row {.tabset data-height=50}
-----------------------
  
<center>

<font size="6">**Pruned unfiltered SNPS**</font>

</center>
  
Row {.tabset data-height=600}
-----------------------
  
### maf = 0
  
```{r}
pca=PCA_list$Prune_unfiltered$maf0[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.05

```{r}
pca=PCA_list$Prune_unfiltered$maf0.05[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.1

```{r}
pca=PCA_list$Prune_unfiltered$maf0.1[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.15

```{r}
pca=PCA_list$Prune_unfiltered$maf0.15[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.20

```{r}
pca=PCA_list$Prune_unfiltered$maf0.2[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.25

```{r}
pca=PCA_list$Prune_unfiltered$maf0.25[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.30

```{r}
pca=PCA_list$Prune_unfiltered$maf0.3[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.35

```{r}
pca=PCA_list$Prune_unfiltered$maf0.35[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.40

```{r}
pca=PCA_list$Prune_unfiltered$maf0.4[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.45

```{r}
pca=PCA_list$Prune_unfiltered$maf0.45[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.50

```{r}
pca=PCA_list$Prune_unfiltered$maf0.5[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

Sarda sarda {data-navmenu="Species"}
=======================================================================
  
```{r, include = FALSE}
load(file = paste(path,"/output/pca/Ssard_PCA_list.Rdata",sep=""))
```

Row {.tabset data-height=100}
-----------------------
  
<center>

<font size="6">**Sarda sarda**</font>

</center>
  
Row {.tabset data-height=50}
-----------------------

<center>

<font size="6">**All filtered SNPS**</font>

</center>

Row {.tabset data-height=600}
-----------------------
  
### maf = 0
  
```{r}
pca=PCA_list$All_filtered$maf0[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.05

```{r}
pca=PCA_list$All_filtered$maf0.05[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.1

```{r}
pca=PCA_list$All_filtered$maf0.1[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.15

```{r}
pca=PCA_list$All_filtered$maf0.15[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.20

```{r}
pca=PCA_list$All_filtered$maf0.2[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.25

```{r}
pca=PCA_list$All_filtered$maf0.25[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.30

```{r}
pca=PCA_list$All_filtered$maf0.3[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.35

```{r}
pca=PCA_list$All_filtered$maf0.35[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.40

```{r}
pca=PCA_list$All_filtered$maf0.4[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.45

```{r}
pca=PCA_list$All_filtered$maf0.45[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.50

```{r}
pca=PCA_list$All_filtered$maf0.5[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

Row {.tabset data-height=50}
-----------------------
  
<center>

<font size="6">**Pruned filtered SNPS**</font>

</center>
  
Row {.tabset data-height=600}
-----------------------
  
### maf = 0
  
```{r}
pca=PCA_list$Prune_filtered$maf0[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.05

```{r}
pca=PCA_list$Prune_filtered$maf0.05[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.1

```{r}
pca=PCA_list$Prune_filtered$maf0.1[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.15

```{r}
pca=PCA_list$Prune_filtered$maf0.15[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.20

```{r}
pca=PCA_list$Prune_filtered$maf0.2[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.25

```{r}
pca=PCA_list$Prune_filtered$maf0.25[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.30

```{r}
pca=PCA_list$Prune_filtered$maf0.3[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.35

```{r}
pca=PCA_list$Prune_filtered$maf0.35[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.40

```{r}
pca=PCA_list$Prune_filtered$maf0.4[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.45

```{r}
pca=PCA_list$Prune_filtered$maf0.45[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.50

```{r}
pca=PCA_list$Prune_filtered$maf0.5[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

Row {.tabset data-height=50}
-----------------------
  
<center>

<font size="6">**All unfiltered SNPS**</font>

</center>
  
Row {.tabset data-height=600}
-----------------------
  
### maf = 0
  
```{r}
pca=PCA_list$All_unfiltered$maf0[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.05

```{r}
pca=PCA_list$All_unfiltered$maf0.05[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.1

```{r}
pca=PCA_list$All_unfiltered$maf0.1[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.15

```{r}
pca=PCA_list$All_unfiltered$maf0.15[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.20

```{r}
pca=PCA_list$All_unfiltered$maf0.2[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.25

```{r}
pca=PCA_list$All_unfiltered$maf0.25[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.30

```{r}
pca=PCA_list$All_unfiltered$maf0.3[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.35

```{r}
pca=PCA_list$All_unfiltered$maf0.35[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.40

```{r}
pca=PCA_list$All_unfiltered$maf0.4[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.45

```{r}
pca=PCA_list$All_unfiltered$maf0.45[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.50

```{r}
pca=PCA_list$All_unfiltered$maf0.5[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

Row {.tabset data-height=50}
-----------------------
  
<center>

<font size="6">**Pruned unfiltered SNPS**</font>

</center>
  
Row {.tabset data-height=600}
-----------------------
  
### maf = 0
  
```{r}
pca=PCA_list$Prune_unfiltered$maf0[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.05

```{r}
pca=PCA_list$Prune_unfiltered$maf0.05[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.1

```{r}
pca=PCA_list$Prune_unfiltered$maf0.1[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.15

```{r}
pca=PCA_list$Prune_unfiltered$maf0.15[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.20

```{r}
pca=PCA_list$Prune_unfiltered$maf0.2[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.25

```{r}
pca=PCA_list$Prune_unfiltered$maf0.25[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.30

```{r}
pca=PCA_list$Prune_unfiltered$maf0.3[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.35

```{r}
pca=PCA_list$Prune_unfiltered$maf0.35[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.40

```{r}
pca=PCA_list$Prune_unfiltered$maf0.4[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.45

```{r}
pca=PCA_list$Prune_unfiltered$maf0.45[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.50

```{r}
pca=PCA_list$Prune_unfiltered$maf0.5[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

Syngnathus typhle {data-navmenu="Species"}
=======================================================================
  
```{r, include = FALSE}
load(file = paste(path,"/output/pca/Styph_PCA_list.Rdata",sep=""))
```

Row {.tabset data-height=100}
-----------------------
  
<center>

<font size="6">**Syngnathus typhle**</font>

</center>
  
Row {.tabset data-height=50}
-----------------------

<center>

<font size="6">**All filtered SNPS**</font>

</center>

Row {.tabset data-height=600}
-----------------------
  
### maf = 0
  
```{r}
pca=PCA_list$All_filtered$maf0[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.05

```{r}
pca=PCA_list$All_filtered$maf0.05[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.1

```{r}
pca=PCA_list$All_filtered$maf0.1[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.15

```{r}
pca=PCA_list$All_filtered$maf0.15[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.20

```{r}
pca=PCA_list$All_filtered$maf0.2[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.25

```{r}
pca=PCA_list$All_filtered$maf0.25[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.30

```{r}
pca=PCA_list$All_filtered$maf0.3[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.35

```{r}
pca=PCA_list$All_filtered$maf0.35[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.40

```{r}
pca=PCA_list$All_filtered$maf0.4[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.45

```{r}
pca=PCA_list$All_filtered$maf0.45[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.50

```{r}
pca=PCA_list$All_filtered$maf0.5[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

Row {.tabset data-height=50}
-----------------------
  
<center>

<font size="6">**Pruned filtered SNPS**</font>

</center>
  
Row {.tabset data-height=600}
-----------------------
  
### maf = 0
  
```{r}
pca=PCA_list$Prune_filtered$maf0[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.05

```{r}
pca=PCA_list$Prune_filtered$maf0.05[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.1

```{r}
pca=PCA_list$Prune_filtered$maf0.1[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.15

```{r}
pca=PCA_list$Prune_filtered$maf0.15[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.20

```{r}
pca=PCA_list$Prune_filtered$maf0.2[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.25

```{r}
pca=PCA_list$Prune_filtered$maf0.25[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.30

```{r}
pca=PCA_list$Prune_filtered$maf0.3[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.35

```{r}
pca=PCA_list$Prune_filtered$maf0.35[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.40

```{r}
pca=PCA_list$Prune_filtered$maf0.4[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.45

```{r}
pca=PCA_list$Prune_filtered$maf0.45[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.50

```{r}
pca=PCA_list$Prune_filtered$maf0.5[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

Row {.tabset data-height=50}
-----------------------
  
<center>

<font size="6">**All unfiltered SNPS**</font>

</center>
  
Row {.tabset data-height=600}
-----------------------
  
### maf = 0
  
```{r}
pca=PCA_list$All_unfiltered$maf0[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.05

```{r}
pca=PCA_list$All_unfiltered$maf0.05[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.1

```{r}
pca=PCA_list$All_unfiltered$maf0.1[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.15

```{r}
pca=PCA_list$All_unfiltered$maf0.15[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.20

```{r}
pca=PCA_list$All_unfiltered$maf0.2[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.25

```{r}
pca=PCA_list$All_unfiltered$maf0.25[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.30

```{r}
pca=PCA_list$All_unfiltered$maf0.3[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.35

```{r}
pca=PCA_list$All_unfiltered$maf0.35[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.40

```{r}
pca=PCA_list$All_unfiltered$maf0.4[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.45

```{r}
pca=PCA_list$All_unfiltered$maf0.45[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.50

```{r}
pca=PCA_list$All_unfiltered$maf0.5[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

Row {.tabset data-height=50}
-----------------------
  
<center>

<font size="6">**Pruned unfiltered SNPS**</font>

</center>
  
Row {.tabset data-height=600}
-----------------------
  
### maf = 0
  
```{r}
pca=PCA_list$Prune_unfiltered$maf0[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.05

```{r}
pca=PCA_list$Prune_unfiltered$maf0.05[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.1

```{r}
pca=PCA_list$Prune_unfiltered$maf0.1[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.15

```{r}
pca=PCA_list$Prune_unfiltered$maf0.15[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.20

```{r}
pca=PCA_list$Prune_unfiltered$maf0.2[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.25

```{r}
pca=PCA_list$Prune_unfiltered$maf0.25[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.30

```{r}
pca=PCA_list$Prune_unfiltered$maf0.3[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.35

```{r}
pca=PCA_list$Prune_unfiltered$maf0.35[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.40

```{r}
pca=PCA_list$Prune_unfiltered$maf0.4[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.45

```{r}
pca=PCA_list$Prune_unfiltered$maf0.45[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

### maf = 0.50

```{r}
pca=PCA_list$Prune_unfiltered$maf0.5[[1]]
data_pca=data.frame(INDIV=pca$sample.id,
                    PC1=pca$eigenvect[,1],
                    PC2=pca$eigenvect[,2],
                    PC3=pca$eigenvect[,3],
                    PC4=pca$eigenvect[,4],
                    LOCA=c(rep("Algarve",5),
                           rep("Bay of Biscay",5),
                           rep("Gulf of Lion",5),
                           rep("Costa Calida",5)))

color_med_atl=rev(brewer.pal(n=4,name="RdBu"))
p<-ggplot(data=data_pca,aes(x=PC1,y=PC2,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 1 (",round(pca$varprop[1]*100,2),"% )",sep=""))+
  ylab(paste("PCA 2 (",round(pca$varprop[2]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p1<-p

p<-ggplot(data=data_pca,aes(x=PC3,y=PC4,label=INDIV))+
  theme_minimal()+
  theme(panel.grid=element_blank(),
        panel.border=element_rect(fill="transparent"),
        plot.title=element_text(hjust=0.5))+
  geom_hline(yintercept=0,lty=2)+
  geom_vline(xintercept=0,lty=2)+
  geom_point(size=3,aes(col=LOCA))+
  xlab(paste("PCA 3 (",round(pca$varprop[3]*100,2),"% )",sep=""))+
  ylab(paste("PCA 4 (",round(pca$varprop[4]*100,2),"% )",sep=""))+  
  scale_colour_manual(name="Location",
                      values=c(color_med_atl[2],
                               color_med_atl[1],
                               color_med_atl[3],
                               color_med_atl[4]))
p2<-p

data_varpop=data.frame(PC=factor(paste("P",seq(1,10),sep=""),levels=paste("P",seq(1,10),sep="")),VAR=pca$varprop[1:10])
pp<-ggplot(data_varpop,aes(x=PC,y=VAR))+
  geom_bar(stat='identity',fill="dodgerblue2",alpha=0.25)+
  theme_classic()+
  xlab("Principal Component")+
  ylab("Variation explained (%)")
```

```{r}
subplot(ggplotly(p1)%>% layout(legend = list(orientation = "h", x = 0.2, y =-0.15)), ggplotly(p2)%>%hide_legend(),         ggplotly(pp)%>%hide_legend(),          titleX=T,titleY=T,margin=0.035,widths=c(0.375,0.425,0.2),which_layout=1) %>% partial_bundle()
```

Packages used {data-icon="fa-map"}
=======================================================================

```{r}
installed.packages()[names(sessionInfo()$otherPkgs), "Version"]
```